Q: How to replace "(" with "\(" in the regexp, Emacs/elisp flavor? Question as title.
More specifically, I'm rather tired of having to type \(, etc. every time I want a parenthesis in Emacs's (interactive) regexp functions (not to mention the \\( in code). So I wrote something like
(defadvice query-replace-regexp (before my-query-replace-regexp activate)
   (ad-set-arg 0 (replace-regexp-in-string "(" "\\\\(" (ad-get-arg 0)))
   (ad-set-arg 0 (replace-regexp-in-string ")" "\\\\)" (ad-get-arg 0)))))

in hope that I can conveniently forget about emacs's idiosyncrasy in regexp during "interaction mode". Except I cannot get the regexp right... 
(replace-regexp-in-string "(" "\\\\(" "(abc")

gives \\(abc instead of the wanted \(abc. Other variations on the number of slashes just gives errors. Thoughts?
Since I started questioning, might as well ask another one: since lisp code is not supposed to use interactive functions, advicing query-replace-regexp should be okay, am I correct? 

A: The replacement you has works well for me.
Take the text:
hi there mom
hi son!

and try query-replace-regexp with your advice:
M-x query-replace-regexp (hi).*(mom) RET \1 \2! RET

yields
hi mom!
hi son!

I didn't have to put a backslash in front of the parentheses to get them to group.  That said, this disables being able to match actual parentheses...
The reason the replace-regexp-in-string yields \\(abc, is that as a string, that is equivalent to an interactively typed \(abc.  In a string \ is used to denote that the following character is special, e.g. "\t" is a string with a tab.  So, in order to specify just a backslash, you need to use a backslash in front of it "\\" is a string containing a backslash.
Regarding advising interactive functions, lisp code can call interactive functions all it wants.  A prime example is find-file - which is called all over the place.  To make your advice a little safer, you can wrap the body with a check for interactive-p to avoid mussing with internal calls:
(defadvice query-replace-regexp (before my-query-replace-regexp activate)
  (when (interactive-p)
    (ad-set-arg 0 (replace-regexp-in-string "(" "\\\\(" (ad-get-arg 0)))
    (ad-set-arg 0 (replace-regexp-in-string ")" "\\\\)" (ad-get-arg 0)))))

